Invited Talk

Comparative Genomics: Is It Changing the Paradigm ofEvolutionary Biology?
Eugene V. Koonin

koonin@ncbi.nlm.nih.gov
National Center for Biotechnology Information, National Library of Medicine
National Institutes of Health
Bethesda MD 20894, USA

About 20 complete genome sequences of cellular life forms | bacteria, archaea an eukaryotes |are currently available, and many more are in the pipeline. Considerable comparative analysis of thesegenomes has already been performed, and while even more challenging work lies ahead, it is fair to ask
at this juncture, what is the impact of this research on biology in general. In my opinion, comparativeanalysis of complete genome has already a ected our ideas of what biological evolution is to such anextent that it is appropriate to claim a paradigm shift in evolutionary biology.
Computer analysis of complete genomes of unicellular organisms shows that protein sequences arein general highly conserved in evolution, with at least 70% of them containing ancient conserved regions. This allows us to delineate families of orthologs across a wide phylogenetic range and in manycases, predict protein functions with reasonable con dence. Once a robust set of such orthologousfamilies is established, it is possible to examine the pattern of phylogenetic representation (or forbrevity, simply `phylogenetic pattern') for each of them. Such an examination readily shows that for
the great majority of orthologous families, the phylogenetic distribution is quite patchy and in manycases unexpected. Only 100 families, the majority of them including components of the translation machinery, are universally conserved in all sequenced genomes. These observations indicate thathorizontal gene transfer and lineage-speci c gene loss are not inconsequential evolutionary quirks but
rather prevailing forces of evolution, at least in the prokaryotic world. On many occasions, in detailed
studies of protein superfamilies and even entire functional systems, such as those for DNA repair andprogrammed cell death, it is now possible to reconstruct detailed evolutionary scenarios that accountfor a number of distinct events of horizontal gene transfer and gene loss. These detailed studies showthat at the level of individual genes, horizontal gene transfer and gene loss are complemented by numerous recombination events that manifest in domain rearrangement at the protein level. Previously,
such rearrangements were associate primarily with exon shuing but the analysis of complete genomes
shows that they are critically important also in the prokaryotic world where this mechanism is notoperative.
Examination of phylogenetic patterns for families of orthologous proteins also results in more
speci c conclusions some of which may have far-reaching consequences. In particular, it is now clearthat the basic DNA replication machineries (that is, the replicative DNA polymerases, primases,
helicases, and several other proteins) in bacteria and in archaea/eukaryotes are not orthologous andmay have evolved independently. This is in a sharp contrast with the remarkable conservation of thecomponents of the translation apparatus and the core transcription machinery. The simplest, even if
unconventional interpretation of these observations is that the common ancestor of all extant cellular
life forms actually had an RNA genome that, however, encoded an advanced translation machinery,
the main proteins currently used for transcription (which at that time might have been involved in218

genome replication) and probably a considerable repertoire of metabolic enzymes. Taking into accountthe common chemical knowledge that long RNA molecules are quite unstable and the conclusions
on the major role of gene sampling discussed above, we arrive to an unexpected, speculative but
not unplausible picture of the common ancestor of all known life (the so-called cenancestor). Thecenancestor might not even have had a de ned genome in the sense all modern organisms have it but
rather could be a loose collection of a large number of relatively small, in a sense virus-like, RNA-based
genetic elements.
Further genome sequencing, particularly of genomes of deep-branching organisms will put theseconcepts to test and in any case, will add more substance for critical analysis. This must be complemented by further developments of methods for theoretical and ultimately experimental analysis ofevolution on the basis of multiple genome comparison.

Acknowledgements
I thank L. Aravind for numerous stimulating discussions, without which these ideas could not havebeen developed in a clear form. I am aware and appreciative of the major contribution of Carl Woeseto our understanding of the possible nature of the Universal Ancestor [5].

References[1] Mushegian, A.R. and Koonin, E.V., A minimal gene set for cellular life derived by comparison ofcomplete bacterial genomes, Proc. Natl. Acad. Sci. U.S.A., 93:10268{10273, 1996.
[2] Koonin, E.V., Mushegian, A.R., Galperin, M.Y., and Walker, D.R., Comparison of archaeal andbacterial genomes: computer analysis of protein sequences predicts novel functions and suggests
a chimeric origin for the archaea, Mol. Microbiol., 25:619{637, 1997.
[3] Tatusov, R.L., Koonin, E.V., and Lipman, D.J., A genomic perspective on protein families,
Science, 278:631{637, 1997.
[4] Huynen, M.A. and Bork, P., Measuring genome evolution, Proc. Natl. Acad. Sci. U.S.A., 95:5849{5856, 1998.
[5] Woese, C. The universal ancestor, Proc. Natl. Acad. Sci. U.S.A., 95:6854{6859, 1998.

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